Phylogeography, Population Structure, and Species Delimitation in Rockhopper Penguins (Eudyptes chrysocome and Eudyptes moseleyi)

Rockhopper penguins are delimited as 2 species, the northern rockhopper (Eudyptes moseleyi) and the southern rockhopper (Eudyptes chrysocome), with the latter comprising 2 subspecies, the western rockhopper (Eudyptes chrysocome chrysocome) and the eastern rockhopper (Eudyptes chrysocome filholi). We conducted a phylogeographic study using multilocus data from 114 individuals sampled across 12 colonies from the entire range of the northern/southern rockhopper complex to assess potential population structure, gene flow, and species limits. Bayesian and likelihood methods with nuclear and mitochondrial DNA, including model testing and heuristic approaches, support E. moseleyi and E. chrysocome as distinct species lineages with a divergence time of 0.97 Ma. However, these analyses also indicated the presence of gene flow between these species. Among southern rockhopper subspecies, we found evidence of significant gene flow and heuristic approaches to species delimitation based on the genealogical diversity index failed to delimit them as species. The best-supported population models for the southern rockhoppers were those where E. c. chrysocome and E. c. filholi were combined into a single lineage or 2 lineages with bidirectional gene flow. Additionally, we found that E. c. filholi has the highest effective population size while E. c. chrysocome showed similar effective population size to that of the endangered E. moseleyi. We suggest that the current taxonomic definitions within rockhopper penguins be upheld and that E. chrysocome populations, all found south of the subtropical front, should be treated as a single taxon with distinct management units for E. c. chrysocome and E. c. filholi.

Colonization and diversification of the white-browed shortwing (Aves: Muscicapidae: Brachypteryx montana) in the Philippines

Molecular phylogenetic approaches have greatly improved our knowledge of the pattern and process of biological diversification across the globe; however, many regions remain poorly documented, even for well-studied vertebrate taxa. The Philippine archipelago, one of the least-studied 'biodiversity hotspots', is an ideal natural laboratory for investigating the factors driving diversification in an insular and geologically dynamic setting. We investigated the history and geography of diversification of the Philippine populations of a widespread montane bird, the White-browed Shortwing (Brachypteryx montana). Leveraging dense archipelago-wide sampling, we generated a multi-locus genetic dataset (one nuclear and two mtDNA markers), which we analyzed using phylogenetic, population genetic, and coalescent-based methods. Our results demonstrate that Philippine shortwings (1) likely colonized the Philippines from the Sunda Shelf to Mindanao in the late Miocene or Pliocene, (2) diversified across inter-island barriers into three divergent lineages during the Pliocene and early Pleistocene, (3) have not diversified within the largest island, Luzon, contrary to patterns observed in other montane taxa, and (4) colonized Palawan from the oceanic Philippines rather than from Borneo, challenging the assumption of Palawan functioning exclusively as a biogeographic extension of the Sunda Shelf. Additionally, our finding that divergent (c. 4.0 mya) lineages are coexisting in secondary sympatry on Mindanao without apparent gene flow suggests that the speciation process is likely complete for these shortwing lineages. Overall, these investigations provide insight into how topography and island boundaries influence diversification within remote oceanic archipelagos and echo the results of many other studies in demonstrating that taxonomic diversity continues to be underestimated in the Philippines.

Genomic Analysis of Demographic History and Ecological Niche Modeling in the Endangered Sumatran Rhinoceros Dicerorhinus sumatrensis

The vertebrate extinction rate over the past century is approximately 22-100 times greater than background extinction rates [1], and large mammals are particularly at risk [2, 3]. Quaternary megafaunal extinctions have been attributed to climate change [4], overexploitation [5], or a combination of the two [6]. Rhinoceroses (Family: Rhinocerotidae) have a rich fossil history replete with iconic examples of climate-induced extinctions [7], but current pressures threaten to eliminate this group entirely. The Sumatran rhinoceros (Dicerorhinus sumatrensis) is among the most imperiled mammals on earth. The 2011 population was estimated at ≤216 wild individuals [8], and currently the species is extirpated, or nearly so, throughout the majority of its former range [8-12]. Understanding demographic history is important in placing current population status into a broader ecological and evolutionary context. Analysis of the Sumatran rhinoceros genome reveals extreme changes in effective population size throughout the Pleistocene. Population expansion during the early to middle Pleistocene was followed by decline. Ecological niche modeling indicated that changing climate most likely played a role in the decline of the Sumatran rhinoceros, as less suitable habitat on an emergent Sundaland corridor isolated Sumatran rhinoceros populations. By the end of the Pleistocene, the Sundaland corridor was submerged, and populations were fragmented and consequently reduced to low Holocene levels from which they would never recover. Past events denuded the Sumatran rhinoceros of genetic diversity through population decline, fragmentation, or some combination of the two and most likely made the species even more susceptible to later exploitation and habitat loss. VIDEO ABSTRACT.

Discovery of the elusive leptin in birds: identification of several 'missing links' in the evolution of leptin and its receptor

Leptin is a pleiotropic protein best known for regulation of appetite and fat storage in mammals. While many leptin orthologs have been identified among vertebrates, an authentic leptin in birds has remained elusive and controversial. Here we identify leptin sequence from the Peregrine falcon, Falco peregrinus (pfleptin), and identify sequences from two other birds (mallard and zebra finch), and 'missing' vertebrates (elephant shark, alligator, Indian python, Chinese soft-shelled turtle, and coelacanth). The pattern of genes surrounding leptin (snd1, rbm28) is syntenic between the falcon and mammalian genomes. Phylogenetic analysis of all known leptin protein sequences improves our understanding of leptin's evolution. Structural modeling of leptin orthologs highlights a highly conserved hydrophobic core in the four-helix cytokine packing domain. A docked model of leptin with the leptin receptor for Peregrine falcon reveals several conserved amino acids important for the interaction and possible coevolution of leptin with its receptor. We also show for the first time, an authentic avian leptin sequence that activates the JAK-STAT signaling pathway. These newly identified sequences, structures, and tools for avian leptin and its receptor will allow elucidation of the function of these proteins in feral and domestic birds.

An empirical comparison of character-based and coalescent-based approaches to species delimitation in a young avian complex

The process of discovering species is a fundamental responsibility of systematics. Recently, there has been a growing interest in coalescent-based methods of species delimitation aimed at objectively identifying species early in the divergence process. However, few empirical studies have compared these new methods with character-based approaches for discovering species. In this study, we applied both a character-based and a coalescent-based approaches to delimit species in a closely related avian complex, the light-vented/Taiwan bulbul (Pycnonotus sinensis/Pycnonotus taivanus). Population aggregation analyses of plumage, mitochondrial and 13 nuclear intron character data sets produced conflicting species hypotheses with plumage data suggesting three species, mitochondrial data suggesting two species, and nuclear intron data suggesting one species. Such conflict is expected among recently diverged species, and by integrating all sources of data, we delimited three species verified with independently congruent character evidence as well as a more weakly supported fourth species identified by a single character. Attempts to validate species hypothesis using Bayesian Phylogenetics and Phylogeography (BPP), a coalescent-based method of species delimitation, revealed several issues that can seemingly affect statistical support for species recognition. We found that θ priors had a dramatic impact on speciation probabilities, with lower values consistently favouring splitting and higher values consistently favouring lumping. More resolved guide trees also resulted in overall higher speciation probabilities. Finally, we found suggestive evidence that BPP is sensitive to the divergent effects of nonrandom mating caused by intraspecific processes such as isolation-with-distance, and therefore, BPP may not be a conservative method for delimiting independently evolving population lineages. Based on these concerns, we questioned the reliability of BPP results and based our conclusions about species limits exclusively on character data.

Recent range-wide demographic expansion in a Taiwan endemic montane bird, Steere's Liocichla (Liocichla steerii)

Background

The subtropical island of Taiwan is an area of high endemism and a complex topographic environment. Phylogeographic studies indicate that vicariance caused by Taiwan's mountains has subdivided many taxa into genetic phylogroups. We used mitochondrial DNA sequences and nuclear microsatellites to test whether the evolutionary history of an endemic montane bird, Steere's Liocichla (Liocichla steerii), fit the general vicariant paradigm for a montane organism.

Results

We found that while mountains appear to channel gene flow they are not a significant barrier for Steere's Liocichla. Recent demographic expansion was evident, and genetic diversity was relatively high across the island, suggesting expansion from multiple areas rather than a few isolated refugia. Ecological niche modeling corroborated the molecular results and suggested that populations of Steere's Liocichla are connected by climatically suitable habitat and that there was less suitable habitat during the Last Glacial Maximum.

Conclusions

Genetic and ecological niche modeling data corroborate a single history--Steere's Liocichla was at lower density during the Last Glacial Maximum and has subsequently expanded in population density. We suggest that such a range-wide density expansion might be an overlooked cause for the genetic patterns of demographic expansion that are regularly reported. We find significant differences among some populations in F_ST indices and an admixture analysis. Though both of these results are often used to suggest conservation action, we affirm that statistically significant results are not necessarily biologically meaningful and we urge caution when interpreting highly polymorphic data such as microsatellites.

Tests of spatial and temporal factors influencing extra-pair paternity in red-winged blackbirds

Extra-pair paternity (EPP) is a widespread and highly variable reproductive phenomenon in birds. We tested the effects of habitat, spatial factors, and timing of breeding on the occurrence of EPP in red-winged blackbirds (Agelaius phoeniceus). We used PCR-amplified microsatellites to assess the paternity of 1479 nestlings from 537 broods on 235 territories over four breeding seasons. Over 4 years, 40% of nestlings were extra-pair. At least 27% of actual sires were non-neighbours, suggesting that males or females interacted over longer distances than in other populations of red-winged blackbirds. The level of EPP was significantly clumped within broods and males but not within females across broods. EPP was negatively related to the area of a male's territory. The spatial proximity of a female's nest to the territory boundary had no effect on total EPP, but tended to increase the probability of an EPP by a nearby male. We found no influence on EPP of the type of habitat on the territory or the level of nesting activity nearby. The time in the season when a nest was started and the synchrony of breeding also had no significant effect on the level of EPP. The age of the male, the age of his neighbours, and the interaction between the two had no effect on total EPP. However, older males were less likely to have an offspring sired by a neighbour on their territory. Males with older neighbours were also less likely to have offspring sired by a neighbour, particularly if they were new territory owners. The high variability in who gained and lost paternity, and the limited impact of spatial and temporal factors influencing it, have some interesting implications for theories seeking to explain mating patterns.

Choosing mates: good genes versus genes that are a good fit

Female choice for male ornamental traits is widely accepted as a mechanism by which females maximize their reproductive success and/or offspring quality. However, there is an increasing empirical literature that shows a fitness benefit of genetic diversity and a tendency for females to use genetic dissimilarity as a criterion for mate choice. This genetic compatibility hypothesis for female mate choice presents a paradox. How can females use both an absolute criterion, such as male ornamentation, and a relative criterion, such as genetic dissimilarity, to choose their mates? Here, we present potential solutions for this dilemma and the empirical evidence supporting them. The interplay between these two contrasting forms of female mate choice presents an exciting empirical and theoretical challenge for evolutionary ecologists.

Concordant evolution of plumage colour, feather microstructure and a melanocortin receptor gene between mainland and island populations of a fairy-wren

Studies of the patterns of diversification of birds on islands have contributed a great deal to the development of evolutionary theory. In white-winged fairy-wrens, Malurus leucopterus, mainland males develop a striking blue nuptial plumage whereas those on nearby islands develop black nuptial plumage. We explore the proximate basis for this divergence by combining microstructural feather analysis with an investigation of genetic variation at the melanocortin-1 receptor locus (MC1R). Fourier analysis revealed that the medullary keratin matrix (spongy layer) of the feather barbs of blue males was ordered at the appropriate nanoscale to produce the observed blue colour by coherent light scattering. Surprisingly, the feather barbs of black males also contained a spongy layer that could produce a similar blue colour. However, black males had more melanin in their barbs than blue males, and this melanin may effectively mask any structural colour produced by the spongy layer. Moreover, the presence of this spongy layer suggests that black island males evolved from a blue-plumaged ancestor. We also document concordant patterns of variation at the MC1R locus, as five amino acid substitutions were perfectly associated with the divergent blue and black plumage phenotypes. Thus, with the possible involvement of a melanocortin receptor locus, increased melanin density may mask the blue-producing microstructure in black island males, resulting in the divergence of plumage coloration between mainland and island white-winged fairy-wrens. Such mechanisms may also be responsible for plumage colour diversity across broader geographical and evolutionary scales.

The effect of vegetation density on male mate guarding and extra-territorial forays in the yellow-breasted chat (Icteria virens)

Extra-pair paternity is widely documented in birds, but the behaviors that lead to extra-pair copulations (EPCs) have been less well studied, particularly in territorial songbirds. We studied the behaviors associated with extra-territorial forays (ETFs) and male mate guarding in a socially monogamous, but genetically promiscuous, neotropical migrant passerine, the yellow-breasted chat (Icteria virens). Focal observations and radiotelemetry revealed that both males and females engaged in ETFs. 65% of the females in our study engaged in at least one foray onto a neighboring territory. 50% of males also were observed engaging in ETFs, but males were much more conspicuous during these intrusions compared to females. Females preferred to remain close to the ground in areas where vegetation was the densest. Female behavior was difficult to observe during ETFs but females sometimes interacted with neighboring extra-pair males. Males attempted to guard their mates by remaining close to them and following them during extra-territorial intrusions. We observed instances in which a male attacked his mate and appeared to herd her back to his territory. However a male's ability to maintain close proximity to his mate was significantly and negatively correlated with vegetation density. Our results suggest that the behaviors which lead to extra-pair encounters are influenced by the behavior of all participants and are modified by the characteristics of the habitat.

Molecular Variability of House Finch Mycoplasma gallisepticum Isolates as Revealed by Sequencing and Restriction Fragment Length Polymorphism Analysis of the pvpA Gene

Mycoplasma gallisepticum, a major pathogen of chickens and turkeys, has caused significant declines in house finch (Carpodacus mexicanus) populations in the eastern United States since it was first observed in this species in 1994. There is evidence that M. gallisepticum infection is now endemic among eastern house finches, although disease prevalence has declined, suggesting an evolving host-parasite relationship. Studies based on randomly amplified polymorphic DNA (RAPD) have documented the presence of a single, unique RAPD profile in house finch M. gallisepticum isolates, suggesting a single point source of origin, which agrees with the known epidemiologic observations. In the present study, we evaluated the molecular variability of 55 house finch isolates as well as 11 chicken and turkey isolates including reference strains of M. gallisepticum. Molecular variability was evaluated by polymerase chain reaction (PCR)-restriction fragment length polymorphism (RFLP) analysis and nucleotide sequencing of the pvpA gene, which encodes for the putative cytadhesin protein PvpA. Three different RFLP groups and 16 genotypes were evident from the 55 house finch isolates evaluated. Sequence analysis of pvpA gene PCR products showed that although most house finch M. gallisepticum isolates clustered more closely to each other, others clustered more closely to either turkey or chicken field isolates. These findings suggest that house finch isolates are more polymorphic than previously recognized by RAPD studies. This feature may allow us to learn more about the molecular evolution and epidemiology of this emerging disease host-parasite relationship.